Files in venelin/PCMBase
Simulation and Likelihood Calculation of Phylogenetic Comparative Models

.Rbuildignore
.gitattributes
.gitignore
.travis.yml
DESCRIPTION
NAMESPACE
NEWS.md
PCMBase.Rproj
R/AutoGeneratedModelTypes.R R/BM.R R/BMdrift.R R/DOU.R R/DefaultModelTypes.R R/GaussianPCM.R R/JOU.R R/LatexTools.R R/MixedGaussian.R R/OU.R R/PCM.R R/PCMBaseTestObjects.R R/PCMParam.R R/PCMTable.R R/PCMTree.R R/Utilities.R R/White.R R/matrixparametrizations.R R/zzz.R README.Rmd README.md
_pkgdown.yml
codecov.yml
cran-comments.md
data-raw/.gitignore
data-raw/.replace_function_names.sh
data-raw/CreateTestObjects.R data-raw/Fig1.pdf
data-raw/Fig1.tex
data-raw/Fig1Simplified.Rmd
data-raw/Fig1Simplified.tex
data-raw/Fig3.Rmd
data-raw/Fig3TableModels.tex
data-raw/TestsForListCladePartitions.R
data-raw/TreeMGPMExample.tex
data-raw/TreeMGPMSimplified.tex
data/PCMBaseTestObjects.rda
data/dataFig3.rda
docs/articles/Fig1.pdf
docs/articles/PCMBase.html
docs/articles/PCMBase_files/figure-html/unnamed-chunk-10-1.png
docs/articles/PCMBase_files/figure-html/unnamed-chunk-14-1.png
docs/articles/PCMBase_files/figure-html/unnamed-chunk-8-1.png
docs/articles/PCMBase_files/figure-html/unnamed-chunk-9-1.png
docs/articles/PCMCreateModel.html
docs/articles/PCMCreateModel_files/figure-html/unnamed-chunk-9-1.png
docs/articles/PCMParam.html
docs/articles/PCMTracePruning.html
docs/articles/index.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/favicon.ico
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Args_MixedGaussian_MGPMDefaultModelTypes.html
docs/reference/Args_MixedGaussian_MGPMScalarOUType.html
docs/reference/Args_MixedGaussian_MGPMSurfaceOUType.html
docs/reference/FormatCellAsLatex.html
docs/reference/FormatTableAsLatex.html
docs/reference/MGPMScalarOUType.html
docs/reference/MGPMSurfaceOUType.html
docs/reference/MixedGaussian.html
docs/reference/PCM.html
docs/reference/PCMAbCdEf.html
docs/reference/PCMApplyTransformation.html
docs/reference/PCMBaseIsADevRelease.html
docs/reference/PCMBaseTestObjects.html
docs/reference/PCMColorPalette.html
docs/reference/PCMCond.GaussianPCM.html
docs/reference/PCMCond.html
docs/reference/PCMCondVOU.html
docs/reference/PCMCreateLikelihood.html
docs/reference/PCMDefaultModelTypes.html
docs/reference/PCMDefaultObject.html
docs/reference/PCMDescribe.html
docs/reference/PCMDescribeParameters.html
docs/reference/PCMExtractDimensions.html
docs/reference/PCMExtractRegimes.html
docs/reference/PCMFindMethod.html
docs/reference/PCMFixParameter.html
docs/reference/PCMGenerateModelTypes.html
docs/reference/PCMGenerateParameterizations.html
docs/reference/PCMGetVecParamsRegimesAndModels.html
docs/reference/PCMInfo.html
docs/reference/PCMLik.html
docs/reference/PCMLikDmvNorm.html
docs/reference/PCMLikTrace.html
docs/reference/PCMListParameterizations.html
docs/reference/PCMLmr.html
docs/reference/PCMMapModelTypesToRegimes.html
docs/reference/PCMMean.html
docs/reference/PCMMeanAtTime.html
docs/reference/PCMModelTypes.html
docs/reference/PCMModels.html
docs/reference/PCMNumRegimes.html
docs/reference/PCMNumTraits.html
docs/reference/PCMOptions.html
docs/reference/PCMPExpxMeanExp.html
docs/reference/PCMPLambdaP_1.html
docs/reference/PCMPairSums.html
docs/reference/PCMParam.html
docs/reference/PCMParamCount.html
docs/reference/PCMParamGetShortVector.html
docs/reference/PCMParamLoadOrStore.html
docs/reference/PCMParamLocateInShortVector.html
docs/reference/PCMParamLowerLimit.html
docs/reference/PCMParamRandomVecParams.html
docs/reference/PCMParamSetByName.html
docs/reference/PCMParamType.html
docs/reference/PCMParamUpperLimit.html
docs/reference/PCMParentClasses.html
docs/reference/PCMParseErrorMessage.html
docs/reference/PCMPlotGaussianDensityGrid2D.html
docs/reference/PCMPlotGaussianSample2D.html
docs/reference/PCMPlotMath.html
docs/reference/PCMPlotTraitData2D.html
docs/reference/PCMPresentCoordinates.html
docs/reference/PCMRegimes.html
docs/reference/PCMSim.html
docs/reference/PCMSpecify.html
docs/reference/PCMTable.html
docs/reference/PCMTableParameterizations.html
docs/reference/PCMTrajectory-1.png
docs/reference/PCMTrajectory-2.png
docs/reference/PCMTrajectory.html
docs/reference/PCMTree-1.png
docs/reference/PCMTree-2.png
docs/reference/PCMTree-3.png
docs/reference/PCMTree.html
docs/reference/PCMTreeBackbonePartition-1.png
docs/reference/PCMTreeBackbonePartition-10.png
docs/reference/PCMTreeBackbonePartition-2.png
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docs/reference/PCMTreeBackbonePartition.html
docs/reference/PCMTreeDropClade-1.png
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docs/reference/PCMTreeDropClade.html
docs/reference/PCMTreeDtNodeParts.html
docs/reference/PCMTreeDtNodeRegimes.html
docs/reference/PCMTreeDtNodes.html
docs/reference/PCMTreeEdgeTimes.html
docs/reference/PCMTreeEvalNestedEDxOnTree-1.png
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docs/reference/PCMTreeEvalNestedEDxOnTree.html
docs/reference/PCMTreeExtractBackboneRegimes.html
docs/reference/PCMTreeExtractClade-1.png
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docs/reference/PCMTreeExtractClade-3.png
docs/reference/PCMTreeExtractClade.html
docs/reference/PCMTreeGetBranchLength.html
docs/reference/PCMTreeGetDaughters.html
docs/reference/PCMTreeGetLabels.html
docs/reference/PCMTreeGetParent.html
docs/reference/PCMTreeGetPartNames.html
docs/reference/PCMTreeGetPartRegimes.html
docs/reference/PCMTreeGetPartition.html
docs/reference/PCMTreeGetPartsForNodes.html
docs/reference/PCMTreeGetRegimeForNode.html
docs/reference/PCMTreeGetRegimesForEdges.html
docs/reference/PCMTreeGetRegimesForNodes.html
docs/reference/PCMTreeGetStartingNodesRegimes.html
docs/reference/PCMTreeGetTipsInPart-1.png
docs/reference/PCMTreeGetTipsInPart.html
docs/reference/PCMTreeGetTipsInRegime-1.png
docs/reference/PCMTreeGetTipsInRegime.html
docs/reference/PCMTreeInsertSingletons-1.png
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docs/reference/PCMTreeInsertSingletons.html
docs/reference/PCMTreeJumps.html
docs/reference/PCMTreeListAllPartitions-1.png
docs/reference/PCMTreeListAllPartitions.html
docs/reference/PCMTreeListCladePartitions.html
docs/reference/PCMTreeListDescendants.html
docs/reference/PCMTreeListRootPaths.html
docs/reference/PCMTreeLocateEpochOnBranches.html
docs/reference/PCMTreeLocateMidpointsOnBranches.html
docs/reference/PCMTreeMatchLabels.html
docs/reference/PCMTreeMatchRegimesWithModel.html
docs/reference/PCMTreeMatrixNodesInSamePart.html
docs/reference/PCMTreeMatrixNodesInSameRegime.html
docs/reference/PCMTreeMatrixTipsInSameRegime.html
docs/reference/PCMTreeNearestNodesToEpoch.html
docs/reference/PCMTreeNodeTimes.html
docs/reference/PCMTreeNumNodes.html
docs/reference/PCMTreeNumParts.html
docs/reference/PCMTreeNumTips.html
docs/reference/PCMTreeNumUniqueRegimes.html
docs/reference/PCMTreePlot.html
docs/reference/PCMTreePostorder.html
docs/reference/PCMTreePreorder.html
docs/reference/PCMTreeSetDefaultRegime.html
docs/reference/PCMTreeSetLabels.html
docs/reference/PCMTreeSetPartRegimes-1.png
docs/reference/PCMTreeSetPartRegimes-2.png
docs/reference/PCMTreeSetPartRegimes.html
docs/reference/PCMTreeSetPartition-1.png
docs/reference/PCMTreeSetPartition-2.png
docs/reference/PCMTreeSetPartition-3.png
docs/reference/PCMTreeSetPartition.html
docs/reference/PCMTreeSetRegimes.html
docs/reference/PCMTreeSetRegimesForEdges-1.png
docs/reference/PCMTreeSetRegimesForEdges.html
docs/reference/PCMTreeSplitAtNode-1.png
docs/reference/PCMTreeSplitAtNode-2.png
docs/reference/PCMTreeSplitAtNode-3.png
docs/reference/PCMTreeSplitAtNode.html
docs/reference/PCMTreeTableAncestors.html
docs/reference/PCMTreeToString.html
docs/reference/PCMTreeUniqueRegimes.html
docs/reference/PCMTreeVCV.html
docs/reference/PCMUnfixParameter.html
docs/reference/PCMVar.html
docs/reference/PCMVarAtTime.html
docs/reference/TruePositiveRate.html
docs/reference/UpperChol.html
docs/reference/White.html
docs/reference/dataFig3.html
docs/reference/index.html
docs/reference/is.MixedGaussian.html
docs/reference/is.PCM.html
docs/reference/is.PCMTree.html
docs/sitemap.xml
inst/CITATION
man/Args_MixedGaussian_MGPMDefaultModelTypes.Rd man/Args_MixedGaussian_MGPMScalarOUType.Rd man/Args_MixedGaussian_MGPMSurfaceOUType.Rd man/FormatCellAsLatex.Rd man/FormatTableAsLatex.Rd man/MGPMScalarOUType.Rd man/MGPMSurfaceOUType.Rd man/MatchListMembers.Rd man/MixedGaussian.Rd man/PCM.Rd man/PCMAbCdEf.Rd man/PCMAddToListAttribute.Rd man/PCMApplyTransformation.Rd man/PCMBaseIsADevRelease.Rd man/PCMBaseTestObjects.Rd man/PCMColorPalette.Rd man/PCMCombineListAttribute.Rd man/PCMCond.GaussianPCM.Rd man/PCMCond.Rd man/PCMCondVOU.Rd man/PCMCreateLikelihood.Rd man/PCMDefaultModelTypes.Rd man/PCMDefaultObject.Rd man/PCMDescribe.Rd man/PCMDescribeParameters.Rd man/PCMExtractDimensions.Rd man/PCMExtractRegimes.Rd man/PCMFindMethod.Rd man/PCMFixParameter.Rd man/PCMGenerateModelTypes.Rd man/PCMGenerateParameterizations.Rd man/PCMGetAttribute.Rd man/PCMGetVecParamsRegimesAndModels.Rd man/PCMInfo.Rd man/PCMLik.Rd man/PCMLikDmvNorm.Rd man/PCMLikTrace.Rd man/PCMListMembers.Rd man/PCMListParameterizations.Rd man/PCMLmr.Rd man/PCMMapModelTypesToRegimes.Rd man/PCMMean.Rd man/PCMMeanAtTime.Rd man/PCMModelTypes.Rd man/PCMModels.Rd man/PCMNumRegimes.Rd man/PCMNumTraits.Rd man/PCMOptions.Rd man/PCMPExpxMeanExp.Rd man/PCMPLambdaP_1.Rd man/PCMPairSums.Rd man/PCMParam.Rd man/PCMParamCount.Rd man/PCMParamGetShortVector.Rd man/PCMParamLoadOrStore.Rd man/PCMParamLocateInShortVector.Rd man/PCMParamLowerLimit.Rd man/PCMParamRandomVecParams.Rd man/PCMParamSetByName.Rd man/PCMParamType.Rd man/PCMParamUpperLimit.Rd man/PCMParentClasses.Rd man/PCMParseErrorMessage.Rd man/PCMPlotGaussianDensityGrid2D.Rd man/PCMPlotGaussianSample2D.Rd man/PCMPlotMath.Rd man/PCMPlotTraitData2D.Rd man/PCMPresentCoordinates.Rd man/PCMRegimes.Rd man/PCMSetAttribute.Rd man/PCMSim.Rd man/PCMSpecify.Rd man/PCMTable.Rd man/PCMTableParameterizations.Rd man/PCMTrajectory.Rd man/PCMTree.Rd man/PCMTreeBackbonePartition.Rd man/PCMTreeDropClade.Rd man/PCMTreeDtNodes.Rd man/PCMTreeEdgeTimes.Rd man/PCMTreeEvalNestedEDxOnTree.Rd man/PCMTreeExtractClade.Rd man/PCMTreeGetBranchLength.Rd man/PCMTreeGetDaughters.Rd man/PCMTreeGetLabels.Rd man/PCMTreeGetParent.Rd man/PCMTreeGetPartNames.Rd man/PCMTreeGetPartRegimes.Rd man/PCMTreeGetPartition.Rd man/PCMTreeGetPartsForNodes.Rd man/PCMTreeGetRegimesForEdges.Rd man/PCMTreeGetRegimesForNodes.Rd man/PCMTreeGetTipsInPart.Rd man/PCMTreeGetTipsInRegime.Rd man/PCMTreeInsertSingletons.Rd man/PCMTreeJumps.Rd man/PCMTreeListAllPartitions.Rd man/PCMTreeListCladePartitions.Rd man/PCMTreeListDescendants.Rd man/PCMTreeListRootPaths.Rd man/PCMTreeLocateEpochOnBranches.Rd man/PCMTreeLocateMidpointsOnBranches.Rd man/PCMTreeMatchLabels.Rd man/PCMTreeMatrixNodesInSamePart.Rd man/PCMTreeNearestNodesToEpoch.Rd man/PCMTreeNodeTimes.Rd man/PCMTreeNumNodes.Rd man/PCMTreeNumParts.Rd man/PCMTreeNumTips.Rd man/PCMTreePlot.Rd man/PCMTreePostorder.Rd man/PCMTreePreorder.Rd man/PCMTreeSetLabels.Rd man/PCMTreeSetPartRegimes.Rd man/PCMTreeSetPartition.Rd man/PCMTreeSetRegimesForEdges.Rd man/PCMTreeSplitAtNode.Rd man/PCMTreeTableAncestors.Rd man/PCMTreeToString.Rd man/PCMTreeVCV.Rd man/PCMUnfixParameter.Rd man/PCMVar.Rd man/PCMVarAtTime.Rd man/TruePositiveRate.Rd man/UpperTriFactor.Rd man/White.Rd man/dataFig3.Rd man/is.MixedGaussian.Rd man/is.PCM.Rd man/is.PCMTree.Rd tests/PosteriorQuantileTests/BM/BayesValidateBM.R
tests/PosteriorQuantileTests/BM/bsub.sh
tests/PosteriorQuantileTests/DOU/BayesValidateDOU.R
tests/PosteriorQuantileTests/DOU/BayesValidateDOU.RData
tests/PosteriorQuantileTests/DOU/Tree.RData
tests/PosteriorQuantileTests/DOU/bsub.sh
tests/PosteriorQuantileTests/DOU/lsf.o57137962
tests/PosteriorQuantileTests/ExplorePCMModelParams.Rmd tests/PosteriorQuantileTests/JOU/BayesValidateJOU.R
tests/PosteriorQuantileTests/JOU/Tree.RData
tests/PosteriorQuantileTests/JOU/bsub.sh
tests/PosteriorQuantileTests/JOU/lsf.o57226328
tests/PosteriorQuantileTests/JOU/lsf.o57245593
tests/PosteriorQuantileTests/OU/BayesValidateOU.R
tests/PosteriorQuantileTests/OU/bsub.sh
tests/PosteriorQuantileTests/PosteriorQuantileAnalysis.Rmd tests/PosteriorQuantileTests/PosteriorQuantileAnalysis.pdf tests/PosteriorQuantileTests/PosteriorQuantileCommon.R tests/PosteriorQuantileTests/old/JOU/GenSaveTree.R tests/PosteriorQuantileTests/old/JOU/postQuantileTools.R tests/PosteriorQuantileTests/old/JOU/runReplication.R tests/PosteriorQuantileTests/old/TwoSpeedOU/PosteriorQuantilesTwoSpeedOU.R tests/PosteriorQuantileTests/old/TwoSpeedOU/postQuantileTools.R tests/PosteriorQuantileTests/old/TwoSpeedOU/runReplication.R
tests/README.txt
tests/benchmark/testExpm.R tests/testthat.R
tests/testthat/.gitignore
tests/testthat/test-MixedGaussian.R tests/testthat/test-PCM.R tests/testthat/test-PCMLik-BM.R tests/testthat/test-PCMLik-BMdrift.R tests/testthat/test-PCMLik-DOU.R tests/testthat/test-PCMLik-OU.R tests/testthat/test-PCMParam.R tests/testthat/test-PCMSim.R tests/testthat/test-PCMTree.R tests/testthat/test-Transformations.R
vignettes/.gitignore
vignettes/Fig1.pdf vignettes/PCMBase.Rmd vignettes/PCMCreateModel.Rmd vignettes/PCMParam.Rmd vignettes/PCMTracePruning.Rmd
vignettes/REFERENCES-R.bib
vignettes/REFERENCES.bib
venelin/PCMBase documentation built on Nov. 13, 2019, 11:20 p.m.